POLYMERASE CHAIN REACTION LUCIA DHIANTIKA WITASARI 1 dhiantika.staff.ugm.ac.id
Polymerase Chain Reaction
Tehnik PCR merupakan metode amplifikasi(penggandaan) fragmen DNA secara in vitro.
PCR is an iterative process, consisting of three elements:
1. denaturation of the template by heat2. annealing of the oligonucleotide primers to the
single‐stranded target sequence(s)3. extension of the annealed primers by a
thermostable DNA polymerase.
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Essential Components of Polymerase Chain Reactions
• A thermostable DNA polymerase to catalyze template‐dependent synthesis of DNA. • Taq polymerase
• Primers : A pair of synthetic oligonucleotides to prime DNA synthesis.
• Deoxynucleoside triphosphates (dNTPs) • dATP, dTTP, dCTP, and dGTP
• Divalent cations• All thermostable DNA polymerases require free divalent cations — usually Mg2+
for activity.
• Buffer to maintain pH• Tris‐Cl, adjusted to a pH between 8.3 and 8.8 at room temperature,
• Monovalent cations• KCl
• Template DNA
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Primer Design
Length: 16 to 25 bases; rarely for efficient amplification is there a need to
use longer primers.
GC content: should mirror the content of the amplicon. The 3' end should be "weak"; no G or C as the end base.
T m : should be balanced, annealing temperatures are usually 5° to 10°C lower than the T m .– The melting temperatures of oligos (generally valid for oligos in the 18–24 base
range) can be estimated using the formula:
Tm = 2(A+T) + 4(G+C).
Absence of complementarity: 3'‐end, primer‐dimer, internal hairpin structures.
Orientation and placement: important more in RT‐PCR experiments (placement at the 3' or 5' end, or spanning intron/exon junctions)
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A. Double strand DNA
B. Denature96º
50º
C. Anneal primers
50º
D. Polymerase binds
72ºTaq
Taq
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72ºTaq
Taq
E. Copy strands
1
2
3
4
F. Denature
96º
First round of cDNA
synthesis (4 strands)
Taq
Taq
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1
2
3
4
Taq
Taq
Taq
Taq
I. Copy strands
72º
Second round of cDNA
synthesis (8 strands)
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1
2
3
4
72º
K. Bind polymerase (not shown) and copy strands
Third round of cDNA
synthesis (16
strands)
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1
23
4
M. Copy strands at 72º
Fourth round of cDNA
synthesis (32
strands)
72º
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1
23
4
After 5 rounds there are 32
double strands of which 24 (75%) are
are same size
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RT‐PCR
Reverse transcriptase (RT)-PCR adalah amplifikasi fragmen DNA yang diperoleh dari fragmen mRNA. Produk yang dihasilkan adalah cDNA.
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Double strand cDNA
AAAAA
TTTTTRT
AAAAA
TTTTTRT
RTAAAAA
TTTTT
Oligo dT primer is bound to mRNA
Reverse transcriptase (RT) copies first cDNA
strand
Reverse transcriptase digests and
displaces mRNA and copies second strand of cDNA
Conversion of mRNA to cDNA by Reverse Transcription
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Amplifikasi frgamen DNA yang sudah diklonkan kedalam vektor denganmenggunakan primer yang mengenali urutan nukleotida pada vektor.